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MeltSim: The DNA Melting Simulator Since 1980

Overview: The DNA Melting Algorithm

MeltSim is a statistical-mechanical program for calculating melting (denaturation) curves (derivative profiles) and maps of DNA, from genes to genomes. The model is the one-dimensional Ising lattice to which loop entropy has been appended [1][2][3]. The original algorithm is that of Poland & Scheraga [4] and Poland [5], with the Fixman & Friere approximation of the loop entropy by a sum of exponentials [6]. Parameters in Poland's original algorithm were evaluated by Blake & Delcourt [7][8] and provide near-quantitative agreement between observed and calculated Tm, amplitudes, breadths, and areas of transitions obtained under equilibrium conditions.